Spatiotemporal coordination of signaling at single molecule resolution

Advances in live-cell single-molecule imaging and modeling over the past decade have invited the closer study of biological structure and dynamics at the nanoscale. The higher resolution of these single-molecule experiments results in finely-grained datasets that can feed detailed quantitative models. Likewise, single-molecule models can account for microscopic details such as noise and heterogeneity inherent to diffusional and chemical processes, which are often neglected in models based on bulk concentrations. Examining microscale biological structures at single molecule resolution in living cells has led to new findings, such as the dynamic regulation of nanoscale structure. I cover three topics from the perspective of single molecules. Chapters 1-3 are on modeling the spatiotemporal coordination of both spontaneous and pheromone-guided yeast polarity establishment. Chapter 4 is on computational modeling and analysis for a technique called Binder/Tag, which we applied to study the conformational dynamics of the protein Src kinase in living cells. Chapter 5 is on modeling clustering-mediated activation of immunoreceptors, using the phagocytic receptor FcγRIIA as a prototypical example.Doctor of Philosoph

Simulated Yeast with Mobile Polarity Sites Is More Sensitive to Pheromone Gradients

Cell polarity is the asymmetric distribution of cellular components and molecules. It is crucially important for effective cell motility and other directional functions. However, practically all types of cells were exposed in a large amount of molecular noise which interfered cell polarity, leading the cells to polarize in the wrong direction. Interestingly, though exposed in molecular noise, yeast cells can usually find and polarize in the direction of extracellular pheromone gradients during mating. This study investigated how yeast cells decoded the extracellular pheromone gradient to polarize in the right direction despite the noise. With particle-based simulations, we found that when exposed to a shallow signal gradient, the simulated yeast with mobile polarity sites interpreted the direction of the signal more accurately than the one with static polarity sites. Therefore, the highly dynamic polarity sites could help yeast cells to decode the extracellular pheromone gradient against molecular noise. Future studies will focus on adding more complex signaling pathways to the simulated yeast models to further investigate the effect of mobile polarity sites on yeast polarity establishment.Bachelor of Scienc

The Dynamics of Dorsal Actin Waves

The recent years have shown that waves of actin polyermization are central to the morphodynamics of cells. This thesis is dedicated to deciphering of the propagation mechanism underlying actin waves known as Circular Dorsal Ruffles (CDRs). While these ring-shaped undulations on the dorsal cell side have been known to the biological community for several decades the mechanism underlying their formation and propagation has remained a puzzle. It is the hypothesis of this work that CDRs can be described as waves that form and propagate in an active medium that is constituted by the actin machinery of the cell. The identification of the corresponding functional elements is the aim of this work. For this, the structure, morphology and dynamics of CDRs are investigated in detail and with a view that is guided by the typical structure of models of active media. Throughout the whole thesis, the FitzHugh-Nagumo system serves as a prototype model for the explanation of the mechanisms underlying the phenomena observed for CDRs on an abstract level. Novel results are presented regarding the identification of the processes of actin dynamics within CDRs and their compartmentalization. The systematic analysis of the dynamics of CDR wavefronts reveals that they exhibit a number of previously unknown phenomena, among them breathing modes, spiral waves, and collision annihilation. All these features are well founded in the framework of active media. Since the dynamics of CDRs strongly depends on the cellular morphology, a novel method for their investigation is developed in which cells are forced into disc-shapes via microcontact printing for a quantitative analysis of data of identically shaped cells. This framework allows for direct comparability to numerical studies, which reveals that stochastic elements in protein dynamics are key for the understanding of CDRs

Chemical Kinetics

Chemical Kinetics relates to the rates of chemical reactions and factors such as concentration and temperature, which affects the rates of chemical reactions. Such studies are important in providing essential evidence as to the mechanisms of chemical processes. The book is designed to help the reader, particularly students and researchers of physical science, understand the chemical kinetics mechanics and chemical reactions. The selection of topics addressed and the examples, tables and graphs used to illustrate them are governed, to a large extent, by the fact that this book is aimed primarily at physical science (mainly chemistry) technologists. Undoubtedly, this book contains "must read" materials for students, engineers, and researchers working in the chemistry and chemical kinetics area. This book provides valuable insight into the mechanisms and chemical reactions. It is written in concise, self-explanatory and informative manner by a world class scientists in the field

Establishment and maintenance of cell polarity in Myxococcus xanthus

Cell polarity, the asymmetric distribution of proteins within cellular space, underlies key processes in all cells. Motile polarized cells have a front-rear polarity axis that can change dynamically in response to external signals. The rod-shaped M. xanthus cells move with well-defined front-rear polarity. In response to signaling by the Frz chemosensory system this polarity is inverted, and cells reverse their direction of movement. Front-rear polarity is established by a polarity module consisting of the small GTPase MglA, its cognate GEF RomR/RomX and GAP MglB. All four proteins localize asymmetrically to the cell poles with RomR/RomX and MglB mostly at the lagging pole and MglA mostly at the leading pole. In response to Frz signaling, the four proteins switch poles and front-rear polarity is inverted. We used a combination of quantitative experiments and data-driven theory to uncover the design principles underlying the emergence of polarity in M. xanthus. By studying each of the polarity proteins in isolation, using RomR as a proxy for the RomR/RomX complex, and their effects as we systematically reconstruct the system, using precise in vivo techniques to quantify subcellular protein localization, we deduced the network of effective interactions between the polarity proteins. At the core of this interaction network are two positive feedbacks whereby RomR stimulates its own polar recruitment and RomR and MglB mutually recruit one another to the poles. At the same time, a negative feedback is established through MglA, which is recruited by RomR but inhibits RomR/MglB mutual recruitment. Moreover, we identify the MglC protein as important for the RomR/MglB positive feedback, allowing the GEF/GAP pairing at the lagging pole and the establishment of the asymmetry. Our results further show that continuous cycling of MglA is crucial for the emergence of polarity and in the regulation of polarity switching during reversals. Through FRAP experiments and Photoactivatble protein fusions, we reveal that MglB, MglC and RomR participate in a tripartite cluster in which turnover is regulated by MglA activity. We rationalize the localization pattern of the GEF and GAP as providing stable asymmetry while remaining responsive and capable of polarity inversions in response to Frz signaling during cellular reversals. Our results not only have implications for the understanding of polarity and motility in M. xanthus but also for dynamic cell polarity more broadly in bacteria as well as in eukaryotic cells

多細胞組織のメゾスコピックレベルでの分解と再構成 : 複雑適応系の非平衡相転移理論に向けて

学位の種別: 課程博士審査委員会委員 : （主査）東京大学准教授 陳 昱, 東京大学教授 飛原 英治, 東京大学教授 奥田 洋司, 東京大学教授 大橋 弘忠, 京都大学准教授 井上 康博University of Tokyo(東京大学

A complex systems approach to education in Switzerland

The insights gained from the study of complex systems in biological, social, and engineered systems enables us not only to observe and understand, but also to actively design systems which will be capable of successfully coping with complex and dynamically changing situations. The methods and mindset required for this approach have been applied to educational systems with their diverse levels of scale and complexity. Based on the general case made by Yaneer Bar-Yam, this paper applies the complex systems approach to the educational system in Switzerland. It confirms that the complex systems approach is valid. Indeed, many recommendations made for the general case have already been implemented in the Swiss education system. To address existing problems and difficulties, further steps are recommended. This paper contributes to the further establishment complex systems approach by shedding light on an area which concerns us all, which is a frequent topic of discussion and dispute among politicians and the public, where billions of dollars have been spent without achieving the desired results, and where it is difficult to directly derive consequences from actions taken. The analysis of the education system's different levels, their complexity and scale will clarify how such a dynamic system should be approached, and how it can be guided towards the desired performance